[gmx-users] editconf and genbox, not enough waters, box not correct size

[Dr. Daniel James White PhD]

Hi all,

we are doing energy minimisation on a large heterodimeric protein
the pdb file used below was made by pdb2gmx from a pdb file made in 
Bodil.
the original pdb file  has 2 chains
the pdb2gmx command used was
pdb2gmx -f a1b1_open_model.pdb -p a1b1.top -o a1b1.pdb


then doing
editconf -f a1b1.pdb -o box.pdb -d 0.5

and

genbox -cp box.pdb -cs -o b4em.pdb

results in several small boxes smaller than the protein structure 
located on parts of the protein, with water in them but the whole 
protein is not solvated.

Shouldn't these commands create a box that contains the whole protein 
with the rest of the space in the box filled with waters?

What are we doing wrong?

cheers

Dan


Dr. Daniel James White BSc. (Hons.) PhD
Cell Biology
Department of biological and environmental science
University of Jyväskylä
Jyväskylä
Finland
+358 (0)14 260 4183 (work)
+358 (0)414740463 (mob)

http://www.chalkie.org.uk
dan at chalkie.org.uk
white at cc.jyu.fi